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Yang L, Sun J, Zhang T, Chu D, Zhou T, Wang X. Comparative transcriptome analysis and HPLC reveal candidate genes associated with synthesis of bioactive constituents in Rheum palmatum complex. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1239-1252. [PMID: 39184557 PMCID: PMC11341509 DOI: 10.1007/s12298-024-01492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/06/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024]
Abstract
Content of bioactive constituents is one of the most important characteristics in Rheum palmatum complex. Increasing ingredient content through genetic breeding is an effective strategy to solve the contradiction between large market demand and resource depletion, but currently hampered by limited understanding of metabolite biosynthesis in rhubarb. In this study, deep transcriptome sequencing was performed to compare roots, stems, and leaves of two Rheum species (PL and ZK) that show different levels of anthraquinone contents. Approximately 0.52 billion clean reads were assembled into 58,782 unigenes, of which around 80% (46,550) were found to be functionally annotated in public databases. Expression patterns of differential unigenes between PL and ZK were thoroughly investigated in different tissues. This led to the identification of various differentially expressed genes (DEGs) involved in shikimate, MEP, MVA, and polyketide pathways, as well as those involved in catechin and gallic acid biosynthesis. Some structural enzyme genes were shown to be significantly up-regulated in roots of ZK with high anthraquinone content, implying potential central roles in anthraquinone synthesis. Taken together, our study provides insights for future functional studies to unravel the mechanisms underlying metabolite biosynthesis in rhubarb. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01492-z.
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Affiliation(s)
- Li Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Jiangyan Sun
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Tianyi Zhang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Dake Chu
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
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Zhang M, Zhang X, Wang R, Zang R, Guo L, Qi T, Tang H, Chen L, Wang H, Qiao X, Wu J, Xing C. Heat-responsive microRNAs participate in regulating the pollen fertility stability of CMS-D2 restorer line under high-temperature stress. Biol Res 2023; 56:58. [PMID: 37941013 PMCID: PMC10634144 DOI: 10.1186/s40659-023-00465-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Anther development and pollen fertility of cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) restorer lines are susceptible to continuous high-temperature (HT) stress in summer, which seriously hinders the large-scale application of "three-line" hybrids in production. Here, integrated small RNA, transcriptome, degradome, and hormone profiling was performed to explore the roles of microRNAs (miRNAs) in regulating fertility stability in mature pollens of isonuclear alloplasmic near-isogenic restorer lines NH and SH under HT stress at two environments. A total of 211 known and 248 novel miRNAs were identified, of which 159 were differentially expressed miRNAs (DEMs). Additionally, 45 DEMs in 39 miRNA clusters (PmCs) were also identified, and most highly expressed miRNAs were significantly induced in SH under extreme HT, especially four MIR482 and six MIR6300 family miRNAs. PmC28 was located in the fine-mapped interval of the Rf1 gene and contained two DEMs, gra-miR482_L-2R + 2 and gma-miR2118a-3p_R + 1_1ss18TG. Transcriptome sequencing identified 6281 differentially expressed genes, of which heat shock protein (HSP)-related genes, such as HSP70, HSP22, HSP18.5-C, HSP18.2 and HSP17.3-B, presented significantly reduced expression levels in SH under HT stress. Through integrating multi-omics data, we constructed a comprehensive molecular network of miRNA-mRNA-gene-KEGG containing 35 pairs of miRNA/target genes involved in regulating the pollen development in response to HT, among which the mtr-miR167a_R + 1, tcc-miR167c and ghr-miR390a, tcc-miR396c_L-1 and ghr-MIR169b-p3_1ss6AG regulated the pollen fertility by influencing ARF8 responsible for the auxin signal transduction, ascorbate and aldarate metabolism, and the sugar and lipid metabolism and transport pathways, respectively. Further combination with hormone analysis revealed that HT-induced jasmonic acid signaling could activate the expression of downstream auxin synthesis-related genes and cause excessive auxin accumulation, followed by a cascade of auxin signal transduction, ultimately resulting in pollen abortion. The results provide a new understanding of how heat-responsive miRNAs regulate the stability of fertility restoration for CMS-D2 cotton under heat stress.
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Affiliation(s)
- Meng Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Ruijie Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Rong Zang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liangliang Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Jianyong Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
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Zang R, Shahzad K, Zhang X, Guo L, Qi T, Tang H, Wang R, Wang H, Qiao X, Zhang M, Wu J, Xing C. Dose effects of restorer gene modulate pollen fertility in cotton CMS-D2 restorer lines via auxin signaling and flavonoid biosynthesis. PLANT CELL REPORTS 2023; 42:1705-1719. [PMID: 37715064 DOI: 10.1007/s00299-023-03053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/12/2023] [Indexed: 09/17/2023]
Abstract
KEY MESSAGE Dose effects of Rf1 gene regulated retrieval mechanism of pollen fertility for CMS-D2 cotton. Cytoplasmic male sterility conditioned by Gossypium harknessii cytoplasm (CMS-D2) is an economical pollination control system for producing hybrid cotton seeds compared to artificial and chemical emasculation methods. However, the unstable restoring ability of restorer lines is a main barrier in the large-scale application of "three-line" hybrid cotton in China. Our phenotypic investigation determined that the homozygous Rf1Rf1 allelic genotype had a stronger ability to generate fertile pollen than the heterozygous Rf1rf1 allelic genotype. To decipher the genetic mechanisms that control the differential levels of pollen fertility, an integrated metabolomic and transcriptomic analysis was performed at two environments using pollen grains of four cotton genotypes differing in Rf1 alleles or cytoplasm. Totally 5,391 differential metabolite features were detected, and 369 specific differential metabolites (DMs) were identified between homozygous and heterozygous Rf1 allelic genotypes with CMS-D2 cytoplasm. In addition, transcriptome analysis identified 2,490 differentially expressed genes (DEGs) and 96 unique hub DEGs with dynamic regulation in this comparative combination. Further integrated analyses revealed that several key DEGs and DMs involved in indole biosynthesis, flavonoid biosynthesis, and sugar metabolism had strong network linkage with fertility restoration. In vitro application of auxin analogue NAA and inhibitor Auxinole confirmed that over-activated auxin signaling might inhibit pollen development, whereas suppressing auxin signaling partially promoted pollen development in CMS-D2 cotton. Our results provide new insight into how the dosage effects of the Rf1 gene regulate pollen fertility of CMS-D2 cotton.
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Affiliation(s)
- Rong Zang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Ruijie Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Jianyong Wu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
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Song X, Zhang M, Shahzad K, Zhang X, Guo L, Qi T, Tang H, Wang H, Qiao X, Feng J, Han Y, Xing C, Wu J. Comparative Transcriptome Profiling of CMS-D2 and CMS-D8 Systems Characterizes Fertility Restoration Genes Network in Upland Cotton. Int J Mol Sci 2023; 24:10759. [PMID: 37445936 DOI: 10.3390/ijms241310759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Resolving the genetic basis of fertility restoration for cytoplasmic male sterility (CMS) can improve the efficiency of three-line hybrid breeding. However, the genetic determinants of male fertility restoration in cotton are still largely unknown. This study comprehensively compared the full-length transcripts of CMS-D2 and CMS-D8 systems to identify potential genes linked with fertility restorer genes Rf1 or Rf2. Target comparative analysis revealed a higher percentage of differential genes in each restorer line as compared to their corresponding sterile and maintainer lines. An array of genes with specific expression in the restorer line of CMS-D2 had functional annotations related to floral development and pathway enrichments in various secondary metabolites, while specifically expressed genes in the CMS-D8 restorer line showed functional annotations related to anther development and pathway enrichment in the biosynthesis of secondary metabolites. Further analysis identified potentially key genes located in the target region of fertility restorer genes Rf1 or Rf2. In particular, Ghir_D05G032450 can be the candidate gene related to restorer gene Rf1, and Ghir_D05G035690 can be the candidate gene associated with restorer gene Rf2. Further gene expression validation with qRT-PCR confirmed the accuracy of our results. Our findings provide useful insights into decoding the potential regulatory network that retrieves pollen fertility in cotton and will help to further reveal the differences in the genetic basis of fertility restoration for two CMS systems.
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Affiliation(s)
- Xiatong Song
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juanjuan Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yang Han
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jianyong Wu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Zhang J, Zhang L, Liang D, Yang Y, Geng B, Jing P, Qu Y, Huang J. ROS accumulation-induced tapetal PCD timing changes leads to microspore abortion in cotton CMS lines. BMC PLANT BIOLOGY 2023; 23:311. [PMID: 37308826 DOI: 10.1186/s12870-023-04317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is the basis of heterosis exploitation. CMS has been used to hybrid production in cotton, but its molecular mechanism remains unclear. CMS is associated with advanced or delayed tapetal programmed cell death (PCD), and reactive oxygen species (ROS) may mediate this process. In this study, we obtained Jin A and Yamian A, two CMS lines with different cytoplasmic sources. RESULTS Compared with maintainer Jin B, Jin A anthers showed advanced tapetal PCD with DNA fragmentation, producing excessive ROS which accumulated around the cell membrane, intercellular space and mitochondrial membrane. The activities of peroxidase (POD) and catalase (CAT) enzymes which can scavenge ROS were significantly decreased. However, Yamian A tapetal PCD was delayed with lower ROS content, and the activities of superoxide dismutase (SOD) and POD were higher than its maintainer. These differences in ROS scavenging enzyme activities may be caused by isoenzyme gene expressions. In addition, we found the excess ROS generated in Jin A mitochondria and ROS overflow from complex III might be the source in parallel with the reduction of ATP content. CONCLUSION ROS accumulation or abrogation were mainly caused by the joint action of ROS generation and scavenging enzyme activities transformation, which led to the abnormal progression of tapetal PCD, affected the development of microspores, and eventually contributed to male sterility. In Jin A, tapetal PCD in advance might be caused by mitochondrial ROS overproduction, accompanied by energy deficiency. The above studies will provide new insights into the cotton CMS and guide the follow-up research ideas.
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Affiliation(s)
- Jinlong Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Li Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Dong Liang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yujie Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Biao Geng
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Panpan Jing
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yunfang Qu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jinling Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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Mo Z, Ke Y, Huang Y, Duan L, Wang P, Luo W, Que Y, Pi K, Zeng S, Liu R. Integrated transcriptome and proteome analysis provides insights into the mechanism of cytoplasmic male sterility (CMS) in tobacco (Nicotiana tabacum L.). J Proteomics 2023; 275:104825. [PMID: 36754348 DOI: 10.1016/j.jprot.2023.104825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/06/2023] [Accepted: 01/15/2023] [Indexed: 02/08/2023]
Abstract
Cytoplasmic male sterility (CMS) is critical in maximizing crop yield and quality by utilizing tobacco heterosis. However, the mechanism of tobacco CMS formation remains unknown. Using paraffin section observation, transcriptome sequencing, and TMT proteomic analysis, this study describes the differences in expression profiles in morphology, transcription, and translation between the sua-CMS tobacco line (MSYY87) and its corresponding maintainer line (YY87). According to the microspore morphology, MSYY87 began to exhibit abnormal microspore development during the early stages of germination and differentiation (androgynous primordium differentiation stage). According to transcriptomic and proteomic analyses, 17 genes/proteins involved in lipid transport/binding and phenylpropane metabolism were significantly down-regulated at both the mRNA and protein levels. Through further analysis, we identified some key genes that may be involved in tobacco male sterility, including β-GLU related to energy metabolism, 4CL and bHLHs related to anther wall formation, nsLTPs related to pollen germination and anther cuticle, and bHLHs related to pollen tapetum degradation. We speculate that the down-regulation of these genes affects the normal physiological metabolism, making tobacco plants show male sterility. SIGNIFICANCE: Cytoplasmic male sterility (CMS) plays a vital role in utilizing tobacco heterosis and enhancing crop yield and quality. We observed paraffin sections and conducted transcriptome sequencing and mitochondrial proteomics to examine the tobacco CMS line Yunyan 87 (MSYY87) and its maintainer line Yunyan 87 (YY87). The down-regulation expression of β-GLU resulted in insufficient ATP supply, which resulted in disordered energy metabolism. The down-regulation expression of 4CL, nsLTPs and bHLHs may affect the formation of anther wall and anther cuticle, pollen germination, as well as the degradation of pollen tapetum. These various abnormal physiological processes, the male sterility of tobacco is finally caused. The findings shed light on the molecular mechanisms of tobacco CMS and serve as a model for fertility research in other flowering plants.
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Affiliation(s)
- Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Yuzhou Ke
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Ying Huang
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Pingsong Wang
- College of Agriculture, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Wen Luo
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Yuanhui Que
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Kai Pi
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Shuaibo Zeng
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, China; Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China.
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Wang H, Cheng Q, Zhai Z, Cui X, Li M, Ye R, Sun L, Shen H. Transcriptomic and Proteomic Analyses of Celery Cytoplasmic Male Sterile Line and Its Maintainer Line. Int J Mol Sci 2023; 24:ijms24044194. [PMID: 36835607 PMCID: PMC9967367 DOI: 10.3390/ijms24044194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 02/22/2023] Open
Abstract
Male sterility is a common phenomenon in the plant kingdom and based on the organelles harboring the male-sterility genes, it can be classified into the genic male sterility (GMS) and the cytoplasmic male sterility (CMS). In every generation, CMS can generate 100% male-sterile population, which is very important for the breeders to take advantage of the heterosis and for the seed producers to guarantee the seed purity. Celery is a cross-pollinated plant with the compound umbel type of inflorescence which carries hundreds of small flowers. These characteristics make CMS the only option to produce the commercial hybrid celery seeds. In this study, transcriptomic and proteomic analyses were performed to identify genes and proteins that are associated with celery CMS. A total of 1255 differentially expressed genes (DEGs) and 89 differentially expressed proteins (DEPs) were identified between the CMS and its maintainer line, then 25 genes were found to differentially expressed at both the transcript and protein levels. Ten DEGs involved in the fleece layer and outer pollen wall development were identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, most of which were down-regulated in the sterile line W99A. These DEGs and DEPs were mainly enriched in the pathways of "phenylpropanoid/sporopollenin synthesis/metabolism", "energy metabolism", "redox enzyme activity" and "redox processes". Results obtained in this study laid a foundation for the future investigation of mechanisms of pollen development as well as the reasons for the CMS in celery.
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Affiliation(s)
- Haoran Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Ziqi Zhai
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Xiangyun Cui
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Mingxuan Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Ruiquan Ye
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
- Correspondence: (L.S.); (H.S.); Tel.: +86-10-6273-1014 (L.S.); +86-10-6273-2831 (H.S.)
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
- Correspondence: (L.S.); (H.S.); Tel.: +86-10-6273-1014 (L.S.); +86-10-6273-2831 (H.S.)
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Zhang J, Wu P, Li N, Xu X, Wang S, Chang S, Zhang Y, Wang X, Liu W, Ma Y, Manghwar H, Zhang X, Min L, Guo X. A male-sterile mutant with necrosis-like dark spots on anthers was generated in cotton. FRONTIERS IN PLANT SCIENCE 2023; 13:1102196. [PMID: 36699851 PMCID: PMC9868585 DOI: 10.3389/fpls.2022.1102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Although conventional hybrid breeding has paved the way for improving cotton production and other properties, it is undoubtedly time and labor consuming, while the cultivation of male sterile line can fix the problem. Here, we induced male sterile mutants by simultaneously editing three cotton EXCESS MICROSPOROCYTES1 (GhEMS1) genes by CRISPR/Cas9. Notably, the GhEMS1 genes are homologous to AtEMS1 genes, which inhibit the production of middle layer and tapetum cells as well, leading to male sterility in cotton. Interestingly, there are necrosis-like dark spots on the surface of the anthers of GhEMS1s mutants, which is different from AtEMS1 mutant whose anther surface is clean and smooth, suggesting that the function of EMS1 gene has not been uncovered yet. Moreover, we have detected mutations in GhEMS1 genes from T0 to T3 mutant plants, which had necrosis-like dark spots as well, indicating that the mutation of the three GhEMS1 genes could be stably inherited. Dynamic transcriptomes showed plant hormone pathway and anther development genetic network were differential expression in mutant and wild-type anthers. And the lower level of IAA content in the mutant anthers than that in the wild type at four anther developmental stages may be the reason for the male sterility. This study not only facilitates the exploration of the basic research of cotton male sterile lines, but also provides germplasms for accelerating the hybrid breeding in cotton.
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Affiliation(s)
- Jun Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Peng Wu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ning Li
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaolan Xu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Songxin Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Siyuan Chang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuping Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xingxing Wang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wangshu Liu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xianlong Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaoping Guo
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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9
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Development of mitochondrial simple sequence repeat markers to simultaneously distinguish cytoplasmic male sterile sources in cotton. Funct Integr Genomics 2022; 23:25. [PMID: 36576593 DOI: 10.1007/s10142-022-00922-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/29/2022]
Abstract
Deleterious effects on anther development and main economy traits caused by sterile genes or cytoplasms are one of the important genetic characteristics of cytoplasmic male sterility (CMS) systems in cotton, which severely hinder the large-scale application of "three-line" hybrids in production. Therefore, distinct characterization of each cytoplasmic type is mandatory to improve the breeding efficiency of cotton hybrids. In this study, four isonuclear-alloplasmic cotton male sterile lines with G. hirsutum (CMS-(AD)1), G. barbadense (CMS-(AD)2), G. harknessii (CMS-D2), and G. trilobum (CMS-D8) cytoplasms were first created by multiple backcrosses with common genotype Shikang126. Then, 64 pairs of mitochondrial simple sequence repeat (mtSSR) markers were designed to explore the mitochondrial DNA diversities among four isonuclear-alloplasmic cotton male sterile lines, and a total of nine pairs of polymorphic mtSSR molecular markers were successfully developed. Polymorphism analysis indicated that mtSSR59 marker correlated to the atp1 gene could effectively divide the CMS-D2, CMS-(AD)1, and CMS-(AD)2 in one category while the CMS-D8 in another category. Further cytological observation and determination of ATP contents also confirmed the accurate classification of CMS-D2 and CMS-D8 lines. Moreover, the mtSSR59 marker was successfully applied in the marker-assisted selection (MAS) for breeding new male sterile lines and precise differentiation or purity identification of different CMS-based "three-line" and conventional cotton hybrids. This study provides new technical measures for classifying various cytoplasmic sterile lines, and our results will significantly improve the efficiency of there-line hybrid breeding in cotton.
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10
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Yang L, Zhao C, Bai Z, Yang L, Schranz ME, Liu S, Bouwmeester K. Comparative transcriptome analysis of compatible and incompatible Brassica napus- Xanthomonas campestris interactions. FRONTIERS IN PLANT SCIENCE 2022; 13:960874. [PMID: 36105711 PMCID: PMC9465390 DOI: 10.3389/fpls.2022.960874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Black rot caused by the vascular pathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) is widespread in Brassicaceae plants and an infectious disease that causes large yield losses in oil seed rape (Brassica napus L.). Improvement of resistance through breeding is a crucial strategy to prevent black rot disease in B. napus, but presently hampered by insufficient understanding of Xcc-Brassica interactions. This study compares two EMS-mutagenized B. napus lines that show contrasting resistance levels to their susceptible progenitor. Patterns of differential gene expression between these B. napus lines were evaluated at three time points post inoculation by comparative RNA-seq analysis. In line with the observed disease phenotypes, the susceptible line ZS9mXccS-1 displayed a steady amount of differentially expressed genes (DEGs) at different time points of infection, whereas the resistant line ZS9mXccR-1 displayed a gradual increase in DEGs throughout the course of infection. Weighted gene co-expression network analysis (WGCNA) pinpointed multiple defense-related hub genes with potential central roles in immunity, including the cell surface receptor genes CRK11 and BIR1, and the associated downstream regulatory genes WRKY11 and PBL30. KEGG analysis of DEGs belonging to two distinct co-expression modules revealed enriched pathways associated with defense, including Ca2+-signaling, receptor-mediated immunity, and phytohormone balance. Taken together, our comparative transcriptome analysis provides new avenues to unravel the mechanisms underlying black rot resistance in B. napus.
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Affiliation(s)
- Li Yang
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zetao Bai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lingli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
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11
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Feng J, Li Y, Zhang J, Zhang M, Zhang X, Shahzad K, Guo L, Qi T, Tang H, Wang H, Qiao X, Lin Z, Xing C, Wu J. Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:930131. [PMID: 35800603 PMCID: PMC9253813 DOI: 10.3389/fpls.2022.930131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Hybrid utilization has proficiently increased crop production worldwide. The cytoplasmic male sterility (CMS) system has emerged as an efficient tool for commercial hybrid cotton seed production. The restorer line with dominant Rf2 gene can restore the fertility of the CMS-D8 sterile line. However, the molecular mechanism of fertility restoration remains unclear in CMS-D8 cotton that limits wider utilization of three-line hybrid breeding. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to understand fertility restoration mechanism of CMS-D8 cotton. In total, 228,106 full-length non-chimeric transcriptome sequences were obtained from anthers of developing flowering buds. The analysis results identified 3,174 novel isoforms, 2,597 novel gene loci, 652 long non-coding RNAs predicted from novel isoforms, 7,234 alternative splicing events, 114 fusion transcripts, and 1,667 genes with alternative polyadenylation. Specially, two novel genes associated with restoration function, Ghir_D05.742.1 and m64033_190821_201011/21103726/ccs were identified and showed significant higher levels of expression in restorer line than sterile and maintainer lines. Our comparative full-length transcriptome analysis provides new insights into the molecular function of Rf2 fertility restorer gene. The results of this study offer a platform for fertility restoration candidate gene discovery in CMS-D8 cotton.
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Affiliation(s)
- Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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12
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Wang R, Ba Q, Zhang L, Wang W, Zhang P, Li G. Comparative analysis of mitochondrial genomes provides insights into the mechanisms underlying an S-type cytoplasmic male sterility (CMS) system in wheat (Triticum aestivum L.). Funct Integr Genomics 2022; 22:951-964. [PMID: 35678921 DOI: 10.1007/s10142-022-00871-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
Cytoplasmic male sterility (CMS) has been widely used in crop cross breeding. There has been much research on wheat CMS. However, the correlation between S-type CMS and mitochondrial genome remains elusive. Herein, we sequenced the mitochondrial genome of wheat CMS line and compared it with the maintainer line. The results showed that the mitochondrial genome of CMS line encoded 26 tRNAs, 8 rRNAs, and 35 protein-coding genes, and the cob encoding complex III in which the protein coding gene is mutated. This protein is known to affect reactive oxygen (ROS) production. The analysis of ROS metabolism in developing anthers showed that the deficiency of antioxidants and antioxidant enzymes in the sterile system aggravated membrane lipid oxidation, resulting in ROS accumulation, and influencing the anther development. Herein, cob is considered as a candidate causative gene sequence for CMS.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Qingsong Ba
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China.
| | - Lanlan Zhang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Weilun Wang
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Pengfei Zhang
- Xiangyang Academy of Agricultural Sciences, Hubei, 441057, People's Republic of China
| | - Guiping Li
- Key Laboratory of Plant Resources and Biology of Anhui Province, School of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
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13
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You J, Li M, Li H, Bai Y, Zhu X, Kong X, Chen X, Zhou R. Integrated Methylome and Transcriptome Analysis Widen the Knowledge of Cytoplasmic Male Sterility in Cotton ( Gossypium barbadense L.). FRONTIERS IN PLANT SCIENCE 2022; 13:770098. [PMID: 35574131 PMCID: PMC9093596 DOI: 10.3389/fpls.2022.770098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
DNA methylation is defined as a conserved epigenetic modification mechanism that plays a key role in maintaining normal gene expression without altering the DNA sequence. Several studies have reported that altered methylation patterns were associated with male sterility in some plants such as rice and wheat, but global methylation profiles and their possible roles in cytoplasmic male sterility (CMS), especially in cotton near-isogenic lines, remain unclear. In this study, bisulfite sequencing technology and RNA-Seq were used to investigate CMS line 07-113A and its near-isogenic line 07-113B. Using integrated methylome and transcriptome analyses, we found that the number of hypermethylated genes in the differentially methylated regions, whether in the promoter region or in the gene region, was more in 07-113A than the number in 07-113B. The data indicated that 07-113A was more susceptible to methylation. In order to further analyze the regulatory network of male sterility, transcriptome sequencing and DNA methylation group data were used to compare the characteristics of near-isogenic lines 07-113A and 07-113B in cotton during the abortion stage. Combined methylation and transcriptome analysis showed that differentially expressed methylated genes were mainly concentrated in vital metabolic pathways including the starch and sucrose metabolism pathways and galactose metabolism. And there was a negative correlation between gene methylation and gene expression. In addition, five key genes that may be associated with CMS in cotton were identified. These data will support further understanding of the effect of DNA methylation on gene expression and their potential roles in cotton CMS.
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Affiliation(s)
- Jingyi You
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Min Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hongwei Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yulin Bai
- Xinjiang Yida Textile Co., Ltd, Urumqi, China
| | - Xuan Zhu
- Dali Bai Autonomous Prefecture Agricultural Science Extension Institute, Dali, China
| | - Xiangjun Kong
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaoyan Chen
- Dali Bai Autonomous Prefecture Agricultural Science Extension Institute, Dali, China
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
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14
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Gao B, Ren G, Wen T, Li H, Zhang X, Lin Z. A super PPR cluster for restoring fertility revealed by genetic mapping, homocap-seq and de novo assembly in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:637-652. [PMID: 34811574 DOI: 10.1007/s00122-021-03990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Rf candidate genes were related to the super D05_PPR-cluster and verified to be individually nonfunctional. Restorer of fertility (Rf) genes of cytoplasmic male sterility (CMS) is commonly found to be PPR (pentatricopeptide repeat) genes, which are mostly located in a cluster of PPR genes with high similarity. Here, Homocap-seq was applied to analyze PPR clusters in 'three lines,' and we found broad variations within the D05_PPR-cluster in a restorer line and deduced that the D05_PPR-cluster was associated with fertility restoration. Genetic mapping of Rf and Homocap-seq analysis of three genotypes in the F2 population validated that the D05_PPR-cluster was the origin of Rf. Three Rf candidates were cloned that were the most actively expressed genes in the D05_PPR-cluster in the restorer line as revealed by their high-depth amplicons. However, further transgenic experiments showed that none of the candidates could restore fertility of the CMS line independently. Then, the members of the brand-new super D05_PPR-cluster in the restorer line, containing 14 full-length PPRs and at least 13 PPR homologous sequences, were identified by long-read resequencing, which validated the effectiveness of variation and expression prediction of Homocap-seq. Additionally, we found that several PPR duplications, including 2 of the 3 Rf candidates, had undergone site-specific selection as potentially important anther development-associated genes. Finally, we proposed that multiple PPRs were coordinately responsible for the fertility restoration of the CMS line.
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Affiliation(s)
- Bin Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gaofeng Ren
- Yueyang Institute of Agricultural Science, Yueyang, 414000, Hunan, China
| | - Tianwang Wen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiping Li
- Yueyang Institute of Agricultural Science, Yueyang, 414000, Hunan, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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15
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Li F, Wang Y, Gao H, Zhang X, Zhuang N. Comparative transcriptome analysis reveals differential gene expression in sterile and fertile rubber tree varieties during flower bud differentiation. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153506. [PMID: 34492526 DOI: 10.1016/j.jplph.2021.153506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Plant male sterility (MS) is an important agronomic trait that provides an efficient tool for hybridization and heterosis utilization of crops. Based on phenotypic and cytological observations, our study performed a multi-comparison transcriptome analysis strategy on multiple sterile and fertile rubber tree varieties using RNA-seq. Compared with the male-fertile varieties, a total of 1590 differentially expressed genes (DEGs) were detected in male-sterile varieties, including 970 up-regulated and 620 down-regulated transcripts in sterile varieties. Key DEGs were further assessed focusing on anther development, microsporogenesis and plant hormone metabolism. Twenty DEGs were selected randomly to validate transcriptome data using quantitative real-time PCR (qRT-PCR). Eleven key genes were subjected to expression pattern analysis using qRT-PCR and fluorescence in situ hybridization. Among them, nine genes, i.e., A6, GAI1, ACA7, TKPR1, CYP704B1, XTH26, MS1, MS35 and MYB33, that regulate callose metabolism, pollen wall formation, tapetum and microspores development were identified as candidate male-sterile genes. These findings provide insights into the molecular mechanism of male sterility in rubber tree.
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Affiliation(s)
- Fei Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Ying Wang
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Heqiong Gao
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Xiaofei Zhang
- Rubber Research Institute, Chinese Academy of Topical Agricultural Sciences, State Center for Rubber Breeding, Danzhou, Hainan, 571737, China
| | - Nansheng Zhuang
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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16
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Zheng H, Wang R, Jiang Q, Zhang D, Mu R, Xu Y, Nnaemeka VE, Mei J, Zhao Y, Cai F, Yu D, Sun Y, Ke L. Identification and functional analysis of a pollen fertility-associated gene GhGLP4 of Gossypium hirsutum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3237-3247. [PMID: 34272568 DOI: 10.1007/s00122-021-03888-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Cotton male fertility-associated gene GhGLP4, encoding a germin-like protein, is essential for anthers development by keeping ROS homeostasis through reducing H2O2 level. Utilization of heterosis is an important way to increase cotton yield and improve fiber quality in hybrid cotton development programs. Male sterility is used in the development of cotton hybrids to reduce the cost of hybrid seed production by eliminating the process of emasculation. From the transcriptome analysis of genic male sterile mutant (ms1) and its background C312 of G. hirsutum, a gene encoding germin-like protein (GhGLP4) was found significantly down-regulated in different developmental stages of ms1 anthers. To explore the gene function in cotton fertility, GhGLP4 was further studied and interfered by virus-induced gene silencing. In the GhGLP4 interfered cotton lines, the expression level of GhGLP4 was significantly decreased in the stamens, and the down-regulation of GhGLP4 resulted in pollen sac closure, stigma exertion, filament shortening, decrease in the number of anthers and complete male sterility. The expression levels of respiratory burst oxidase homologs (Rboh, NADPH oxidase) were significantly altered. Further investigation showed that the SOD activity decreased while the H2O2 content increased in the atypical stamens. These results indicated that GhGLP4 gene affected the cotton anther development through maintenance of ROS homeostasis by H2O2 reduction.
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Affiliation(s)
- Hongli Zheng
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Rongjia Wang
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Qimeng Jiang
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Diandian Zhang
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Rongrong Mu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Yihan Xu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Vitalis E Nnaemeka
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Jun Mei
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Yanyan Zhao
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Fangfang Cai
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Dongliang Yu
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Yuqiang Sun
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China
| | - Liping Ke
- Plant Genomics and Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China.
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17
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Yang X, Ye J, Niu F, Feng Y, Song X. Identification and verification of genes related to pollen development and male sterility induced by high temperature in the thermo-sensitive genic male sterile wheat line. PLANTA 2021; 253:83. [PMID: 33770279 DOI: 10.1007/s00425-021-03601-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Bioinformatic analysis identified the function of genes regulating wheat fertility. Barley stripe mosaic virus-induced gene silencing verified that the genes TaMut11 and TaSF3 are involved in pollen development and related to fertility conversion. Environment-sensitive genic male sterility is of vital importance to hybrid vigor in crop production and breeding. Therefore, it is meaningful to study the function of the genes related to pollen development and male sterility, which is still not fully understand currently. In this study, YanZhan 4110S, a new thermo-sensitive genic male sterility wheat line, and its near-isogenic line YanZhan 4110 were analyzed. Through comparative transcriptome basic bioinformatics and weighted gene co-expression network to further identify some hub genes, the genes TaMut11 and TaSF3 associated with pollen development and male sterility induced by high-temperature were identified in YanZhan 4110S. Further verification through barley stripe mosaic virus-induced gene silencing elucidated that the silencing of TaMut11 and TaSF3 caused pollen abortion, finally resulting in the declination of fertility. These findings provided data on the abortive mechanism in environment-sensitive genic male sterility wheat.
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Affiliation(s)
- Xuetong Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiali Ye
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fuqiang Niu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Tang M, Li Z, Luo D, Wei F, Kashif MH, Lu H, Hu Y, Yue J, Huang Z, Tan W, Li R, Chen P. A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf. PLANT CELL REPORTS 2021; 40:223-236. [PMID: 33128088 DOI: 10.1007/s00299-020-02628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Numbers of critical genes and pathways were found from the levels of transcriptome and metabolome, which were useful information for understanding of kenaf CMS mechanism. Cytoplasmic male sterility (CMS) is a maternally inherited trait in higher plants that leads to the inability to produce or release functional pollen. However, there is lack of comprehensive studies to reveal the molecular basis of CMS occurrence in kenaf. Herein, we performed transcriptome and UPLC-MS-based metabolome analyses in the anthers of a CMS (UG93A) and its maintainer (UG93B) to sort out essential genes and metabolites responding to CMS in kenaf. Transcriptome characterized 7769 differentially expressed genes (DEGs) between these two materials, and pathway enrichment analysis indicated that these DEGs were involved mainly in pentose and glucuronate interconversions, starch and sucrose metabolism, taurine and hypotaurine metabolism. In the metabolome assay, a total of 116 significantly different metabolites (SDMs) were identified between the CMS and its maintainer line, and these SDMs were involved in eight KEGG pathways, including flavone and flavonol biosynthesis, glycerophospholipid metabolism, flavonoid biosynthesis, glycosylphosphatidylinositol-anchor biosynthesi. Integrated analyses of transcriptome and metabolome showed that 50 genes had strong correlation coefficient values (R2 > 0.9) with ten metabolites enriched in six pathways; notably, most genes and metabolites of flavonoid biosynthesis pathways and flavone and flavonol biosynthesis pathways involved in flavonoids biosynthetic pathways were downregulated in CMS compared to those in maintainer. Taken together, the decreased accumulation of flavonoids resulted from the compromised biosynthesis pathways coupled with energy deficiency in the anthers may contribute largely to CMS in UG93A of kenaf.
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Affiliation(s)
- Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Fan Wei
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Wenye Tan
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China.
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Krüger M, Abeyawardana OAJ, Krüger C, Juříček M, Štorchová H. Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion. Cells 2020; 9:cells9122700. [PMID: 33339225 PMCID: PMC7766179 DOI: 10.3390/cells9122700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.
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Affiliation(s)
- Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Oushadee A. J. Abeyawardana
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Department of Horticulture, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague 6-Suchdol, Czech Republic
| | - Claudia Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Miloslav Juříček
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Correspondence: ; Tel.: +420-225-106-828
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Zhao H, Wang J, Qu Y, Peng R, Magwanga RO, Liu F, Huang J. Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background. BMC Genomics 2020; 21:859. [PMID: 33267770 PMCID: PMC7709281 DOI: 10.1186/s12864-020-07261-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Background Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B. Results We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background. Conclusion We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07261-y.
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Affiliation(s)
- Haiyan Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.,School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Jianshe Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.,School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yunfang Qu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Jinling Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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Chen L, Guo H, Chen S, Yang H, Ghouri F, Shahid MQ. Comparative study on cytogenetics and transcriptome between diploid and autotetraploid rice hybrids harboring double neutral genes. PLoS One 2020; 15:e0239377. [PMID: 32986735 PMCID: PMC7521696 DOI: 10.1371/journal.pone.0239377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/06/2020] [Indexed: 11/18/2022] Open
Abstract
Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.
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Affiliation(s)
- Lin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Haibin Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Center of Experimental Teaching for Common Basic Courses, South China Agricultural University, Guangzhou, China
| | - Shuling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Huijing Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- * E-mail:
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Cheng XQ, Zhang XY, Xue F, Zhu SH, Li YJ, Zhu QH, Liu F, Sun J. Characterization and transcriptome analysis of a dominant genic male sterile cotton mutant. BMC PLANT BIOLOGY 2020; 20:312. [PMID: 32620078 PMCID: PMC7333317 DOI: 10.1186/s12870-020-02522-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/24/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Male sterility is an efficient trait for hybrid seed production and germplasm innovation. Until now, most studies on male sterility were on cytoplasmic and recessive genic sterility, with few on dominant genic male sterility, especially in cotton, due to lack of such mutant. RESULTS We discovered a natural male sterile (MS) Sea Island cotton (G. barbadense) mutant. Genetic analysis showed the mutation was caused by a dominant mutation in a single nuclear gene. Comparative cytological observation of anther sections from MS and wild-type (WT) uncovered cellular differences in anther at and after the tetrad stage of pollen mother cells (PMC). In the MS anthers, the outer wall of pollen grains was free of spinules, the tapetum was vacuolated and showed delayed degradation, consequently, no functional pollen grains. Comparison of transcriptomes from meiosis, tetrad, mononuclear and binuclear pollen, and pollen maturation stages identified 13,783 non-redundant differentially expressed genes (DEGs) between MS and WT. Based on the number of DEGs, analyses of enriched GO terms and KEGG pathways, it was evident that significant transcriptomic changes occurred at and after the tetrad stage, consistent with cytological observation, and that the major differences were on metabolism of starch, sucrose, ascorbate, aldarate, alanine, aspartate and glutamate, and biosynthesis of cutin, suberine and wax. WGCNA analysis identified five modules containing 920 genes highly related to anther development, especially the greenyellow module with 54 genes that was highly associated with PMC meiosis and tetrad formation. A NAC transcription factor (Gh_D11G2469) was identified as a hub gene for this module, which warrants further functional characterization. CONCLUSIONS We demonstrated that the MS trait was controlled by a single dominant nuclear gene and caused by delayed tapetum degradation at the tetrad stage. Comparative transcriptome analysis and gene network construction identified DEGs, enriched GO terms and metabolic pathways, and hub genes potentially associated with anther development and the MS trait. These results contribute to our understanding of dominant genic male sterility (DGMS) and provided source for innovation of cotton germplasm.
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Affiliation(s)
- Xin-Qi Cheng
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China
| | - Xin-Yu Zhang
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China
| | - Fei Xue
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China
| | - Shou-Hong Zhu
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China
| | - Yan-Jun Li
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australia
| | - Feng Liu
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China.
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Xinjiang, 832000, Shihezi, China.
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Liu Z, Li S, Li W, Liu Q, Zhang L, Song X. Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2020; 20:10. [PMID: 31910796 PMCID: PMC6947873 DOI: 10.1186/s12870-019-2196-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/10/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular mechanisms related to anther abortion in wheat, which remain unclear at present. RESULTS In this study, five isonuclear alloplasmic male sterile lines (IAMSLs) and their maintainer were investigated. Cytological analysis indicated that the abortion type was identical in IAMSLs, typical and stainable abortion, and the key abortive period was in the binucleate stage. Most of the 1,281 core shared differentially expressed genes identified by transcriptome sequencing compared with the maintainer in the vital abortive stage were involved in the metabolism of sugars, oxidative phosphorylation, phenylpropane biosynthesis, and phosphatidylinositol signaling, and they were downregulated in the IAMSLs. Key candidate genes encoding chalcone--flavonone isomerase, pectinesterase, and UDP-glucose pyrophosphorylase were screened and identified. Moreover, further verification elucidated that due to the impact of downregulated genes in these pathways, the male sterile anthers were deficient in sugar and energy, with excessive accumulations of ROS, blocked sporopollenin synthesis, and abnormal tapetum degradation. CONCLUSIONS Through comparative transcriptome analysis, an intriguing core transcriptome-mediated male-sterility network was proposed and constructed for wheat and inferred that the downregulation of genes in important pathways may ultimately stunt the formation of the pollen outer wall in IAMSLs. These findings provide insights for predicting the functions of the candidate genes, and the comprehensive analysis of our results was helpful for studying the abortive interaction mechanism in CMS wheat.
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Affiliation(s)
- Zihan Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Sha Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Wei Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Qi Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
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Zheng J, Kong X, Li B, Khan A, Li Z, Liu Y, Kang H, Ullah Dawar F, Zhou R. Comparative Transcriptome Analysis between a Novel Allohexaploid Cotton Progeny CMS Line LD6A and Its Maintainer Line LD6B. Int J Mol Sci 2019; 20:ijms20246127. [PMID: 31817342 PMCID: PMC6940886 DOI: 10.3390/ijms20246127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 12/02/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is an important agronomic feature and provides an effective tool for heterosis utilization of crops. This study reports the comparative transcriptomic sketches between a novel allohexaploid cotton progeny CMS line LD6A and its maintainer line LD6B using de novo transcriptome sequencing technology at the pollen abortion stage. A total of 128,901 Unigenes were identified, in which 2007 were upregulated and 11,864 were downregulated. The significantly differentially expressed genes (DEGs) in LD6A show a distant and diverse genetic nature due to their distant hybrid hexaploidy progeny. Further analysis revealed that most of the DEGs participated in the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, histone acetyltransferase activity, sepal development, stigma development, cotyledon development and microsporogenesis. A highly differentially expressed toxic protein, Abrin, was identified in the CMS line LD6A, which can catalyze the inactivation of ribosomes and consequently lead to cell death through the mitochondrial pathway in human cells. Twelve DEGs were selected randomly to validate transcriptome data using quantitative reverse-transcribed PCR (qRT-PCR). This study will contribute to new ideas and foundations related to the molecular mechanism of CMS and the innovation of cotton germplasm resources.
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Affiliation(s)
- Jie Zheng
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Xiangjun Kong
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Bin Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Aziz Khan
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Zhiling Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Yiding Liu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Haodong Kang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
| | - Farman Ullah Dawar
- Department of Zoology, Kohat University of Science and Technology, Kohat 26000, Pakistan;
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China; (J.Z.); (X.K.); (B.L.); (A.K.); (Z.L.); (Y.L.); (H.K.)
- Correspondence:
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Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton. Int J Mol Sci 2019; 20:ijms20236070. [PMID: 31810186 PMCID: PMC6928835 DOI: 10.3390/ijms20236070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H2O2 production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.
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Comparative Transcriptome Analysis Reveals the Cause for Accumulation of Reactive Oxygen Species During Pollen Abortion in Cytoplasmic Male-Sterile Kenaf Line 722HA. Int J Mol Sci 2019; 20:ijms20215515. [PMID: 31694312 PMCID: PMC6862637 DOI: 10.3390/ijms20215515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/02/2019] [Accepted: 11/03/2019] [Indexed: 12/30/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait used for hybrid production in plants, a novel kenaf CMS line 722HA was derived from the thermo-sensitive male-sterile mutant ‘HMS’ by recurrent backcrossing with 722HB. The line 722HA has great potential for hybrid breeding in kenaf. However, the underlying molecular mechanism that controls pollen abortion in 722HA remains unclear, thus limiting the full utilization of this line. To understand the possible mechanism governing pollen abortion in 722HA, cytological, transcriptomic, and biochemical analyses were carried out to compare the CMS line 722HA and its maintainer line 722HB. Cytological observations of the microspore development revealed premature degradation of the tapetum at the mononuclear stage, which resulted in pollen dysfunction. The k-means clustering analysis of differentially expressed genes (DEGs) revealed that these genes are related to processes associated with the accumulation of reactive oxygen species (ROS), including electron transport chain, F1F0-ATPase proton transport, positive regulation of superoxide dismutase (SOD), hydrogen peroxide catabolic, and oxidation-reduction. Biochemical analysis indicated that ROS-scavenging capability was lower in 722HA than in 722HB, resulting in an accumulation of excess ROS, which is consistent with the transcriptome results. Taken together, these results demonstrate that excessive ROS accumulation may affect the normal development of microspores. Our study provides new insight into the molecular mechanism of pollen abortion in 722HA and will promote further studies of kenaf hybrids.
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Li Y, Qin T, Wei C, Sun J, Dong T, Zhou R, Chen Q, Wang Q. Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2019; 20:ijms20205120. [PMID: 31623069 PMCID: PMC6830320 DOI: 10.3390/ijms20205120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/10/2019] [Accepted: 10/12/2019] [Indexed: 12/19/2022] Open
Abstract
Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.
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Affiliation(s)
- Yuqing Li
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830000, China.
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
| | - Tengfei Qin
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
| | - Chunyan Wei
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
| | - Jialiang Sun
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
| | - Tao Dong
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning 530006, China.
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830000, China.
| | - Qinglian Wang
- School of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province/Henan Key Laboratory Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Xinxiang 453003, China.
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Ning L, Wang H, Li D, Lin Z, Li Y, Zhao W, Chao H, Miao L, Li M. Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus. FRONTIERS IN PLANT SCIENCE 2019; 10:252. [PMID: 30886625 PMCID: PMC6409359 DOI: 10.3389/fpls.2019.00252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.
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Affiliation(s)
- Luyun Ning
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Zhiwei Lin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liyun Miao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
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